Laura
Jean Bierut, M.D., is an associate professor, Nancy L. Saccone, Ph.D.,
is an assistant professor, John P. Rice, Ph.D., is a professor, Alison
Goate, D.Phil., is a professor, and Theodore Reich, M.D., is the Samuel
and Mae S. Ludwig Professor, all at Washington University School of
Medicine, St. Louis, Missouri.

Tatiana
Foroud, Ph.D., is an associate professor, Howard Edenberg, Ph.D., is
a Chancellor’s Professor, P. Michael Conneally, PhD., is a distinguished
professor, T. K. Li, M.D.*, is a distinguished professor, and John Nurnberger,
Jr., M.D., Ph.D., is the Joyce and Iver Small Professor of Psychiatry,
all at Indiana University School of Medicine, Indianapolis, Indiana.

Laura
Almasy, Ph.D., is an associate scientist at the Southwest Foundation,
San Antonio, Texas.

Raymond
Crowe, M.D., is the George Winokur Professor at the University of Iowa,
Iowa City, Iowa.

Victor
Hesselbrock, Ph.D., is a professor at the University of Connecticut
Health Center, Farmington, Connecticut.

Bernice
Porjesz, Ph.D., and Henri Begleiter, M.D., are professors at the State
University of New York, Health Sciences Center at Brooklyn, New York.

Marc
A. Schuckit, M.D., is a professor at the University of California–San
Diego, San Diego, California.

Jay
Tischfield, Ph.D., is a professor at Rutgers University, Piscataway,
New Jersey.

The
Collaborative Study on the Genetics of Alcoholism is supported by NIAAA
grant U10–AA–08403. U.S. Public Health Service grant AA–00231
also supported this work.

Alcoholism is a
disease that runs in families and results at least in part from genetic risk
factors. The Collaborative Study on the Genetics of Alcoholism (COGA) is a Federally
funded effort to identify and characterize those genetic factors. The study
involves more than 1,000 alcoholic subjects and their families, with researchers
conducting comprehensive psychological, physiological, electrophysiological,
and genetic analyses of the participants. These analyses have identified several
traits, or phenotypes, that appear to be genetically determined, such as the
presence of alcohol dependence, the level of response to alcohol, the presence
of coexisting depression, or the maximum number of drinks a person consumes
per occasion. Genetic analyses have identified regions on several chromosomes
that are associated with these phenotypes and need to be studied further.Key words: genetic theory
of AODU (alcohol and other drug use); AODR (alcohol and other drug related)
genetic markers; phenotype; chromosome; AOD dependence potential; genetic variance;
genetic trait; comorbidity; major depression; AOD intake per occasion; electroencephalography;
genetic linkage; genetic correlation analysis

Alcohol dependence is a
common, complex disorder that clusters in families. Strong evidence from twin
and adoption studies suggests that alcoholism is in part caused by a genetic
predisposition. (Definitions of the terms “alcoholism” or “alcohol
dependence” are discussed later in this article.) Many other traits that
are associated with the risk for alcoholism also cluster in families and have
genetic underpinnings. These traits, or phenotypes, include a person’s
response to alcohol; the maximum amount of alcohol a person consumes on a single
occasion; and biological measurements, such as brain electrophysiological measures.
Certain psychiatric disorders that commonly co–occur with and may increase
the risk for alcoholism, such as depression, antisocial personality disorder,
or abuse of other drugs, also may be caused partly by genetic factors. Genetic
studies of complex disorders can use analyses of such correlated characteristics
to improve the likelihood of finding genes that are associated with the development
of these disorders. To use this strategy, researchers must conduct comprehensive
assessments in multiple domains (e.g., behavioral responses and physiological
reactions). This approach allows for the examination of multiple characteristics
that may be influenced by the same underlying genes.

The Collaborative Study
on the Genetics of Alcoholism (COGA) is an ambitious research effort funded
by the National Institute on Alcohol Abuse and Alcoholism to elucidate the genetic
factors contributing to the risk of alcoholism. The investigators participating
in this multicenter study have performed genetic studies of alcohol dependence
and several related phenotypes. This article describes the COGA study and the
methods of genetic analyses used in it, presents some of the phenotypes that
were assessed, and includes a brief review of some of the findings regarding
these phenotypes. More detailed information about recent findings of the COGA
study is provided in the sidebar by Edenberg, pp. 214–218, in this issue.

DESIGN OF THE COGA
STUDY

COGA is a large–scale
effort to detect and map, or determine the location of, genes that influence
susceptibility for developing alcohol dependence. To maximize the potential
of success in this project, the study investigators used a strategy that involved
systematic recruitment of a large number of alcohol–dependent patients
and their relatives; comprehensive clinical assessment; and analysis of targeted
biological traits, such as brain wave measurements.

As a first step, the COGA
investigators recruited alcohol–dependent people from chemical dependency
treatment centers. These patients (also called index cases, or probands) as
well as their family members were invited to participate in the study. All participants
were interviewed to assess various domains, including the presence of alcohol
abuse and dependence; other psychiatric disorders (e.g., depression) and other
medical illnesses; the participant’s family history of alcoholism; and
other behaviors. Diagnoses of alcohol dependence and other psychiatric disorders
were established using a structured, comprehensive, diagnostic interview called
the Semi–Structured Assessment for the Genetics of Alcoholism (SSAGA),
which was developed specifically for the COGA study (Bucholz et al. 1994; Hesselbrock
et al. 1999). To be recruited into the COGA study, probands had to meet both
the diagnostic criteria for alcohol dependence specified in the Diagnostic and
Statistical Manual of Mental Disorders, Third Edition, Revised (DSM–III–R)
(American Psychiatric Association [APA] 1987) and the criteria for definite
alcoholism specified by Feighner and colleagues (1972). The recruitment procedures
have been fully described by Begleiter and colleagues (1995).

Overall, the COGA investigators
recruited more than 1,200 probands and their family members, resulting in interviews
of more than 11,000 people. Among those participants, the investigators selected
262 severely affected families—families in which at least 3 interviewed
first–degree relatives1 were diagnosed with alcohol dependence—for
further intensive assessment for genetic studies. (1 First–degree
relatives of a proband are his or her parents, siblings, and children.) More–distant
relatives in these severely affected families were also recruited into this
phase of the study, so that approximately nine people per family participated
in the genetic studies.

For the families recruited
for the genetic analyses, the investigators gathered additional information
from various domains. For example, they collected blood samples from a total
of 2,282 people for further analysis, as described in the following section.
Furthermore, the participants underwent additional biological measurements,
including measurements of brain activity, such as electroencephalograms (EEGs)
and event–related potentials (ERPs). EEGs measure fundamental electrical
brain activity. ERPs are changes in the ongoing electrical brain activity that
occur as a person responds to a stimulus. EEGs and ERPs can be measured reliably,
and there is strong evidence that the patterns of these brain waves are genetically
determined (Porjesz et al. 2002). Both measures allow important assessments
of underlying biological features related to alcoholism. The participants also
completed several questionnaires—for instance, the Self–Rating of
the Effects of Alcohol (SRE) (Schuckit et al. 2001)—to determine their
response to alcohol.

Genetic Analysis

Because the researchers
did not know in advance which chromosomes would carry genetic factors influencing
the development of alcoholism and related phenotypes, the genetic analyses involved
a survey of all chromosomes—that is, the entire genome. To follow the
inheritance of different regions of each chromosome, the researchers used more
than 300 microsatellite markers—short, repeated DNA sequences that exist
in many variants (i.e., alleles) and whose locations on the chromosomes are
known. Every person carries two copies of each marker, one inherited from the
mother and one inherited from the father. Because of their diversity, these
two copies of each marker are likely to differ, allowing researchers to follow
the inheritance of the corresponding chromosomal regions in a family. Such a
genomewide search strategy allows for the discovery of novel genes not previously
considered candidates for influencing alcoholism risk.

The investigators then used
statistical tests to search for relationships between the pattern of inheritance
of the DNA markers and the traits under investigation (e.g., alcohol dependence)
in the study families. If a relationship existed between certain genetic markers
and a given phenotype—for example, if a variant of a marker occurred more
commonly in family members with the phenotype than would be expected by chance—this
served as evidence of genetic linkage.

The investigators used both
qualitative and quantitative analytic techniques in their genetic analyses.
Qualitative techniques are used to assess traits that can only be either present
or absent (e.g., alcohol dependence). One approach chosen in the COGA study
was the affected sibling pair method, which examines the degree to which sibling
pairs, both of whom exhibit the phenotype under investigation, share genetic
markers. This method looks for deviation from the assumption that siblings on
average share 50 percent of their genes. Thus, two affected siblings would share
genetic factors that contribute to a given phenotype more than 50 percent of
the time. Phenotypes studied using this method included alcohol dependence,
low level of response to alcohol, the presence of alcoholism or depression,
and being unaffected by alcoholism (all of these phenotypes are described in
the following sections). The statistical power of these analyses was limited
because they involved only study participants who exhibited the phenotype under
investigation and thus were unable to take advantage of the detailed assessment
available for all study participants.

The second method of genetic
analysis examined quantitative phenotypes—traits that are present to varying
degrees (e.g., the maximum number of drinks a person has consumed per occasion).
The advantage of quantitative methods is that assessments are available on affected
as well as unaffected people; thus, these methods have greater statistical power
because they include more people. Phenotypes studied using quantitative methods
included the severity scale of alcohol dependence, level of response to alcohol,
maximum number of drinks per occasion, and electrophysiological (i.e., EEG and
ERP) measurements.

PHENOTYPES INVESTIGATED
IN THE COGA STUDY

The comprehensive analyses
included in the COGA study allowed for the analysis of numerous phenotypes,
thereby increasing the likelihood that investigators will find relevant genes.
For example, by choosing a phenotype that occurs only in the most severely affected
people, researchers may reduce the generalizability of findings. Conversely,
by focusing on a phenotype that is very common, researchers define an overly
broad study population that may be highly variable (i.e., heterogeneous) with
respect to genetic findings. The following sections summarize some of the phenotypes
included in the COGA analyses. This discussion focuses on phenotypes that demonstrated
linkage with DNA regions on chromosomes 1 and 4. Other analyses, however, also
found linkage of various phenotypes with other chromosomes.

“Alcohol Dependence”
Phenotype

The phenotype of “alcohol
dependence” was studied both as a categorical variable—that is,
whether a person was affected by alcoholism according to the COGA criteria—and
as a quantitative variable (i.e., according to severity). The severity of alcohol
dependence was classified using multiple commonly used sets of diagnostic criteria:

The DSM–III–R
criteria

The criteria specified
in the fourth edition of the DSM (DSM–IV) (APA 1994)

The criteria specified
in the World Health Organization’s International Classification
of Diseases and Related Health Problems, Tenth Revision (ICD–10)
(WHO 1992–1994)

The COGA criteria as
described above (Reich et al. 1998).

These different definitions
of alcoholism represent various grades of severity of the disorder, with DSM–III–R
criteria the least stringent and the ICD–10 criteria the most stringent.
Consequently, the DSM–III–R criteria identify the largest group
of people affected with alcoholism, and the ICD–10 criteria identify the
smallest, most severely affected group.

When the COGA investigators
compared genetic markers among sibling pairs in which both siblings met the
COGA or ICD–10 criteria for alcohol dependence, they identified one DNA
region (i.e., a locus) on chromosome 1 that showed genetic linkage with the
“alcohol dependence” phenotype (Reich et al. 1998; Foroud et al.
2000). Moreover, when the researchers analyzed alcoholism as an underlying quantitative
trait, they found evidence for genetic linkage with a region on chromosome 4
(Williams et al. 1999).

“Low Level of
Response” Phenotype

One characteristic related
to the development of alcohol dependence is the level of subjective response
to alcohol (Schuckit et al. 2001). People who are at high risk of developing
alcoholism (e.g., children of alcoholics) more frequently report that they need
to consume greater amounts of alcohol to feel alcohol’s effects than do
other people. These people are said to have a low level of response to alcohol;
this characteristic is a powerful predictor of the subsequent development of
alcohol dependence, and twin studies have demonstrated that this trait is genetically
influenced.

The COGA investigators assessed
the participants’ response to alcohol using the SRE questionnaire. SRE
scores can be used either categorically or quantitatively. For categorical analyses,
a certain score on the SRE (e.g., the bottom third of the scores) is designated
as a threshold, and people scoring below this value are classified as having
a low response to alcohol. For quantitative measurements, the scores of all
participants are considered and ordered along a continuum from lowest score
(i.e., lowest response to alcohol) to highest score (i.e., highest response).

Qualitative assessments
using the affected sibling design found evidence for genetic linkage of the
“low level of response” phenotype with the same region on chromosome
1 that was linked with the “alcohol dependence” phenotype (Schuckit
et al. 2001). Quantitative measures also found some evidence of linkage; however,
although suggestive, these results were not statistically significant.2
(2 The analyses were not corrected for the participants’ gender,
weight, body mass index, and similar variables.)

“Alcoholism or
Depression” Phenotype

Many alcohol–dependent
people also suffer from major depressive disorder (Nurnberger et al. 2001),
and twin studies suggest that both disorders share some common genetic factors.
Consistent with previous findings, comorbid alcoholism and depression also commonly
occurred in the COGA families. Given the potential genetic relationship between
alcohol dependence and major depressive disorder, the COGA investigators defined
a composite phenotype termed “alcoholism or depression.” Study participants
who met criteria for alcohol dependence, depression, or both disorders were
considered affected with this phenotype. Depression was defined as the presence
of a lifetime history of major depressive disorder or depressive syndrome as
specified in the DSM–III–R. A depressive syndrome is diagnosed in
people who meet the diagnostic criteria for major depressive disorder but in
whom the depression may have been precipitated by heavy alcohol or other drug
use, medications, or other medical illnesses.

The “alcoholism or
depression” phenotype was studied as a qualitative trait using the affected
sibling design—that is, the analysis included sibling pairs in which both
siblings were alcohol dependent and/or suffered from depression. Accordingly,
in contrast to the other sibling analyses reported here, genetic analyses using
this composite phenotype included people who were afflicted with depression
but were not alcohol dependent. Because depression was more common among female
than among male study participants, this analysis resulted in the inclusion
of more sibling pairs with one or two affected sisters.

The genetic analyses found
evidence for genetic linkage between this phenotype and the chromosome 1 locus
that was also linked to alcohol dependence and low level of response to alcohol
(Nurnberger et al. 2001). In fact, of the traits analyzed, the “alcoholism
or depression” phenotype showed the strongest association with that locus.3
(3 This variation in the strength of the association resulted in
part from the different sample sizes used in the different analyses.) The COGA
findings regarding the association between alcoholism and depression are discussed
in more detail in the article by Nurnberger and colleagues, pp. 233–240,
in this issue.

“Unaffected”
Phenotype

The COGA investigators also
defined a phenotype termed “unaffected,” which was assigned to people
who used alcohol but did not meet the criteria for alcohol dependence (Reich
et al. 1998).4 (4 It is important to note that to be evaluated
for the “unaffected” phenotype, study participants had to be current
drinkers; abstinent participants were not included in the analysis of this phenotype.)
Analysis of people with the “unaffected” phenotype, who were relatively
rare in the COGA families, is interesting because these people developed few
or no alcohol–related problems despite living in a family environment
characterized by the presence of several alcoholic family members and, consequently,
excessive alcohol consumption. This suggests that these people may carry genetic
factors that help protect against the development of alcoholism.

The genetic analyses of
the COGA studies provided some evidence of a genetic linkage of the “unaffected”
phenotype with the same region on chromosome 4 that had also been identified
during the quantitative analyses of the “alcohol dependence” phenotype
(Reich et al. 1998). This finding is intriguing because this DNA region is located
near the genes for alcohol dehydrogenase, an enzyme involved in alcohol metabolism.
Some variants of this enzyme have been shown to protect against the development
of alcoholism in Asian populations (Higuchi et al. 1995, 1996) but are less
commonly found in Caucasian populations.

“Maximum Number
of Drinks” Phenotype

Another alcoholism–related
trait assessed in the COGA study was the maximum number of drinks a person ever
consumed in a 24–hour period, which was determined based on the participants’
response to the question, “What is the largest number of drinks you have
ever had in a 24–hour period?” (Saccone et al. 2000). The examination
of this variable was motivated by twin studies that demonstrated a moderate
genetic influence on the maximum number of drinks a person consumes in 24 hours.
The COGA investigators found a significant association in the study participants
between the maximum number of drinks consumed and the risk of developing alcoholism.
Thus, none of the participants who reported drinking a maximum of 2 drinks within
a 24–hour period exhibited any symptoms of problem drinking. However,
the rate of alcoholism increased with increasing maximum amounts of alcohol
consumption in a 24–hour period. For instance, among participants who
reported drinking 9 or more drinks in a 24–hour period, 65 percent of
men and 53 percent of women were diagnosed with alcohol dependence.

The “maximum number
of drinks” phenotype was a quantitative measurement; accordingly, the
genetic analyses included both alcoholic and nonalcoholic people. These analyses
found a genetic linkage between this phenotype and the locus on chromosome 4
that had already shown linkage with the “unaffected” phenotype and
with severity of alcoholism (Saccone et al. 2000).

Electrophysiological
Phenotypes

Several brain electrophysiological
measures, such as EEGs and ERPs, are altered in people with various psychiatric
disorders, including alcoholism (Porjesz and Begleiter 1998). For example, an
ERP brain wave called P300 frequently is smaller in size (i.e., has a lower
amplitude) in alcoholics than in nonalcoholic people. Increasing evidence also
suggests that the variations in brain electrophysiological activity predate
the development of alcoholism. For example, compared with people without a family
history of alcoholism, alterations in EEGs and ERPs exist both in alcohol–dependent
people and in people who are not alcoholic but are at risk for alcoholism because
they are relatives of alcoholics. These electrophysiological measures therefore
represent biological markers that are related to a predisposition for developing
alcoholism. Accordingly, EEGs and ERPs were included in the COGA analyses, particularly
measurements of the P300 brain wave and another ERP brain wave called N400.

The genetic analyses found
that several regions on chromosome 4 were linked to the electrophysiological
phenotypes:

The DNA region that
previously was found to be linked with the “unaffected” and
“maximum number of drinks” phenotypes also showed some genetic
linkage in a combined analysis of alcohol dependence and P300 amplitude
(Williams et al. 1999).

A second region on
chromosome 4 showed evidence of linkage to the amplitudes of the P300 and
N400 waves when the investigators used a different stimulus to elicit the
ERPs (Almasy et al. 2001). This same region appeared to be linked to alterations
in certain EEG measures (Porjesz et al. 2002).

A third area on chromosome
4 showed strong evidence of linkage to changes in another EEG measurement
(Porjesz et al. 2002). This region is of interest because it contains genes
for proteins (i.e., receptors) that interact with a brain chemical called
gamma–aminobutyric acid (GABA), which is responsible for important
aspects of nerve cell activity and influences EEG activity. Further genetic
analyses indicated that a variant of a GABA receptor gene in this area is
associated with changes in EEG activity.

SUMMARY

In the COGA study, researchers
use comprehensive measurements of numerous behavioral and biological traits
associated with alcoholism to conduct a thorough genetic analysis of this complex
disorder. These analyses have identified several chromosomal regions, particularly
on chromosomes 1 and 4, that appear to be linked to several alcohol–related
phenotypes and that are now the targets of more detailed analyses. The fact
that some of these areas appear to be linked with more than one phenotype strengthens
the evidence that genetic factors in these chromosomal regions contribute to
the development of alcoholism.

In the study of complex
diseases such as alcoholism, it is important to perform a complete assessment
of the disorder and its related characteristics. In COGA, there is a close relationship
between the phenotypes studied and the genetic findings. This means that as
the phenotypes of alcoholism and correlated characteristics are modified, linkage
to different chromosomal regions is found. Although alcohol dependence is correlated
with many behavioral features and physiological measurements, genetic linkage
analyses of the traits studied have pointed to different genetic regions related
to these traits. For example, three phenotypes—“alcohol dependence,”
“low level of response” to alcohol, and “alcoholism or depression”—exhibit
genetic linkage with the same area on chromosome 1, although each of these phenotypes
was found in a different subset of participants. This finding suggests that
a genetic factor may be located in the region that contributes to the development
of multiple characteristics, such as alcohol dependence, depression, and a person’s
initial response to alcohol, with the specific effect depending on other accompanying
factors. Several other phenotypes—“unaffected,” “maximum
number of drinks,” alcoholism severity, and the combined analysis of alcohol
dependence and the P300 component of the ERP—show genetic linkage with
a common region on chromosome 4 that is near the genes for alcohol dehydrogenase.

The evaluation of multiple
traits in the COGA study has provided insights into various alcohol–related
behaviors and biological characteristics that are associated with different
underlying genetic factors. Future work in understanding the genetics of alcoholism
requires a continued, thorough assessment of alcohol–related problems
and correlated characteristics. In addition, researchers will have to make progress
in the development of statistical analytic tools and molecular genetics to allow
the study of more complex phenotypes and genetic information.

ACKNOWLEDGMENTS

The Collaborative Study
on the Genetics of Alcoholism includes nine centers where data collection, analysis,
and/or storage take place. H. Begleiter, of the State University of New York,
Health Sciences Center at Brooklyn, is principal investigator, and T. Reich,
of Washington University, is co–principal investigator. The study sites
and their principal investigators and co–investigators are: Indiana University
(T. K. Li; J. Nurnberger, Jr.; P.M. Conneally; H. Edenberg); University of Iowa
(R. Crowe, S. Kuperman); University of California at San Diego (M. Schuckit);
University of Connecticut (V. Hesselbrock); State University of New York, Health
Sciences Center at Brooklyn (B. Porjesz, H. Begleiter); Washington University
in St. Louis (T. Reich, C.R. Cloninger, J. Rice, A. Goate); Howard University
(R. Taylor); Rutgers University (J. Tischfield); and Southwest Foundation (L.
Almasy).

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PORJESZ, B., and BEGLEITER,
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PORJESZ, B.; ALMASY, L.;
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